---
_id: '4474'
abstract:
- lang: eng
text: 'The simulation preorder for labeled transition systems is defined locally,
and operationally, as a game that relates states with their immediate successor
states. Simulation enjoys many appealing properties. First, simulation has a denotational
characterization: system S simulates system I iff every computation tree embedded
in the unrolling of I can be embedded also in the unrolling of S. Second, simulation
has a logical characterization: S simulates I iff every universal branching-time
formula satisfied by S is satisfied also by I. It follows that simulation is a
suitable notion of implementation, and it is the coarsest abstraction of a system
that preserves universal branching-time properties. Third, based on its local
definition, simulation between finite-state systems can be checked in polynomial
time. Finally, simulation implies trace containment, which cannot be defined locally
and requires polynomial space for verification. Hence simulation is widely used
both in manual and in automatic verification. Liveness assumptions about transition
systems are typically modeled using fairness constraints. Existing notions of
simulation for fair transition systems, however, are not local, and as a result,
many appealing properties of the simulation preorder are lost. We propose a new
view of fair simulation by extending the local definition of simulation to account
for fairness: system View the MathML sourcefairly simulates system View the MathML
source iff in the simulation game, there is a strategy that matches with each
fair computation of View the MathML source a fair computation of View the MathML
source. Our definition enjoys a denotational characterization and has a logical
characterization: View the MathML source fairly simulates View the MathML source
iff every fair computation tree (whose infinite paths are fair) embedded in the
unrolling of View the MathML source can be embedded also in the unrolling of View
the MathML source or, equivalently, iff every Fair-∀AFMC formula satisfied by
View the MathML source is satisfied also by View the MathML source (∀AFMC is the
universal fragment of the alternation-free μ-calculus). The locality of the definition
leads us to a polynomial-time algorithm for checking fair simulation for finite-state
systems with weak and strong fairness constraints. Finally, fair simulation implies
fair trace containment and is therefore useful as an efficiently computable local
criterion for proving linear-time abstraction hierarchies of fair systems.'
acknowledgement: We thank Ramin Hojati, Doron Bustan, and the anonymous reviewers
for their comments on this paper.
article_processing_charge: No
article_type: original
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
- first_name: Sriram
full_name: Rajamani, Sriram
last_name: Rajamani
citation:
ama: Henzinger TA, Kupferman O, Rajamani S. Fair simulation. Information and
Computation. 2002;173(1):64-81. doi:10.1006/inco.2001.3085
apa: Henzinger, T. A., Kupferman, O., & Rajamani, S. (2002). Fair simulation.
Information and Computation. Elsevier. https://doi.org/10.1006/inco.2001.3085
chicago: Henzinger, Thomas A, Orna Kupferman, and Sriram Rajamani. “Fair Simulation.”
Information and Computation. Elsevier, 2002. https://doi.org/10.1006/inco.2001.3085.
ieee: T. A. Henzinger, O. Kupferman, and S. Rajamani, “Fair simulation,” Information
and Computation, vol. 173, no. 1. Elsevier, pp. 64–81, 2002.
ista: Henzinger TA, Kupferman O, Rajamani S. 2002. Fair simulation. Information
and Computation. 173(1), 64–81.
mla: Henzinger, Thomas A., et al. “Fair Simulation.” Information and Computation,
vol. 173, no. 1, Elsevier, 2002, pp. 64–81, doi:10.1006/inco.2001.3085.
short: T.A. Henzinger, O. Kupferman, S. Rajamani, Information and Computation 173
(2002) 64–81.
date_created: 2018-12-11T12:09:02Z
date_published: 2002-02-25T00:00:00Z
date_updated: 2023-06-05T07:53:27Z
day: '25'
doi: 10.1006/inco.2001.3085
extern: '1'
intvolume: ' 173'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.sciencedirect.com/science/article/pii/S0890540101930858?via%3Dihub
month: '02'
oa: 1
oa_version: Published Version
page: 64 - 81
publication: Information and Computation
publication_identifier:
issn:
- 0890-5401
publication_status: published
publisher: Elsevier
publist_id: '255'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Fair simulation
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 173
year: '2002'
...
---
_id: '4476'
abstract:
- lang: eng
text: 'One approach to model checking software is based on the abstract-check-refine
paradigm: build an abstract model, then check the desired property, and if the
check fails, refine the model and start over. We introduce the concept of lazy
abstraction to integrate and optimize the three phases of the abstract-check-refine
loop. Lazy abstraction continuously builds and refines a single abstract model
on demand, driven by the model checker, so that different parts of the model may
exhibit different degrees of precision, namely just enough to verify the desired
property. We present an algorithm for model checking safety properties using lazy
abstraction and describe an implementation of the algorithm applied to C programs.
We also provide sufficient conditions for the termination of the method.'
acknowledgement: "We thank Wes Weimer and Jeff Foster for many useful discussions.
\r\n"
article_processing_charge: No
author:
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Ranjit
full_name: Jhala, Ranjit
last_name: Jhala
- first_name: Ritankar
full_name: Majumdar, Ritankar
last_name: Majumdar
- first_name: Grégoire
full_name: Sutre, Grégoire
last_name: Sutre
citation:
ama: 'Henzinger TA, Jhala R, Majumdar R, Sutre G. Lazy abstraction. In: Proceedings
of the 29th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages.
ACM; 2002:58-70. doi:10.1145/503272.503279'
apa: 'Henzinger, T. A., Jhala, R., Majumdar, R., & Sutre, G. (2002). Lazy abstraction.
In Proceedings of the 29th ACM SIGPLAN-SIGACT symposium on Principles of programming
languages (pp. 58–70). Portland, OR, USA: ACM. https://doi.org/10.1145/503272.503279'
chicago: Henzinger, Thomas A, Ranjit Jhala, Ritankar Majumdar, and Grégoire Sutre.
“Lazy Abstraction.” In Proceedings of the 29th ACM SIGPLAN-SIGACT Symposium
on Principles of Programming Languages, 58–70. ACM, 2002. https://doi.org/10.1145/503272.503279.
ieee: T. A. Henzinger, R. Jhala, R. Majumdar, and G. Sutre, “Lazy abstraction,”
in Proceedings of the 29th ACM SIGPLAN-SIGACT symposium on Principles of programming
languages, Portland, OR, USA, 2002, pp. 58–70.
ista: 'Henzinger TA, Jhala R, Majumdar R, Sutre G. 2002. Lazy abstraction. Proceedings
of the 29th ACM SIGPLAN-SIGACT symposium on Principles of programming languages.
POPL: Principles of Programming Languages, 58–70.'
mla: Henzinger, Thomas A., et al. “Lazy Abstraction.” Proceedings of the 29th
ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, ACM,
2002, pp. 58–70, doi:10.1145/503272.503279.
short: T.A. Henzinger, R. Jhala, R. Majumdar, G. Sutre, in:, Proceedings of the
29th ACM SIGPLAN-SIGACT Symposium on Principles of Programming Languages, ACM,
2002, pp. 58–70.
conference:
end_date: 2002-01-18
location: Portland, OR, USA
name: 'POPL: Principles of Programming Languages'
start_date: 2002-01-16
date_created: 2018-12-11T12:09:03Z
date_published: 2002-01-01T00:00:00Z
date_updated: 2023-06-05T07:45:53Z
day: '01'
doi: 10.1145/503272.503279
extern: '1'
language:
- iso: eng
month: '01'
oa_version: None
page: 58 - 70
publication: Proceedings of the 29th ACM SIGPLAN-SIGACT symposium on Principles of
programming languages
publication_identifier:
isbn:
- '9781581134506'
publication_status: published
publisher: ACM
publist_id: '254'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Lazy abstraction
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
year: '2002'
...
---
_id: '4562'
abstract:
- lang: eng
text: We present interface models that describe both the input assumptions of a
component, and its output behavior. By enabling us to check that the input assumptions
of a component are met in a design, interface models provide a compatibility check
for component-based design. When refining a design into an implementation, interface
models require that the output behavior of a component satisfies the design specification
only when the input assumptions of the specification are satisfied, yielding greater
flexibility in the choice of implementations. Technically, our interface models
are games between two players, Input and Output; the duality of the players accounts
for the dual roles of inputs and outputs in composition and refinement. We present
two interface models in detail, one for a simple synchronous form of interaction
between components typical in hardware, and the other for more complex synchronous
interactions on bidirectional connections. As an example, we specify the interface
of a bidirectional bus, with the input assumption that at any time at most one
component has write access to the bus. For these interface models, we present
algorithms for compatibility and refinement checking, and we describe efficient
symbolic implementations.
acknowledgement: This research was supported in part by the AFOSR grant F49620-00-1-0327,
the DARPA grant F33615-00-C-1693, the MARCO grant 98-DT-660, the NSF grant CCR-9988172,
the SRC grant 99-TJ-683.003, and the NSF CAREER award CCR-0132780.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Arindam
full_name: Chakrabarti, Arindam
last_name: Chakrabarti
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Freddy
full_name: Mang, Freddy
last_name: Mang
citation:
ama: 'Chakrabarti A, De Alfaro L, Henzinger TA, Mang F. Synchronous and bidirectional
component interfaces. In: Proceedings of the 14th International Conference
on Computer Aided Verification. Vol 2404. Springer; 2002:414-427. doi:10.1007/3-540-45657-0_34'
apa: 'Chakrabarti, A., De Alfaro, L., Henzinger, T. A., & Mang, F. (2002). Synchronous
and bidirectional component interfaces. In Proceedings of the 14th International
Conference on Computer Aided Verification (Vol. 2404, pp. 414–427). Copenhagen,
Denmark: Springer. https://doi.org/10.1007/3-540-45657-0_34'
chicago: Chakrabarti, Arindam, Luca De Alfaro, Thomas A Henzinger, and Freddy Mang.
“Synchronous and Bidirectional Component Interfaces.” In Proceedings of the
14th International Conference on Computer Aided Verification, 2404:414–27.
Springer, 2002. https://doi.org/10.1007/3-540-45657-0_34.
ieee: A. Chakrabarti, L. De Alfaro, T. A. Henzinger, and F. Mang, “Synchronous and
bidirectional component interfaces,” in Proceedings of the 14th International
Conference on Computer Aided Verification, Copenhagen, Denmark, 2002, vol.
2404, pp. 414–427.
ista: 'Chakrabarti A, De Alfaro L, Henzinger TA, Mang F. 2002. Synchronous and bidirectional
component interfaces. Proceedings of the 14th International Conference on Computer
Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 2404, 414–427.'
mla: Chakrabarti, Arindam, et al. “Synchronous and Bidirectional Component Interfaces.”
Proceedings of the 14th International Conference on Computer Aided Verification,
vol. 2404, Springer, 2002, pp. 414–27, doi:10.1007/3-540-45657-0_34.
short: A. Chakrabarti, L. De Alfaro, T.A. Henzinger, F. Mang, in:, Proceedings of
the 14th International Conference on Computer Aided Verification, Springer, 2002,
pp. 414–427.
conference:
end_date: 2002-07-31
location: Copenhagen, Denmark
name: 'CAV: Computer Aided Verification'
start_date: 2002-07-27
date_created: 2018-12-11T12:09:29Z
date_published: 2002-06-19T00:00:00Z
date_updated: 2023-06-02T12:01:22Z
day: '19'
doi: 10.1007/3-540-45657-0_34
extern: '1'
intvolume: ' 2404'
language:
- iso: eng
month: '06'
oa_version: None
page: 414 - 427
publication: Proceedings of the 14th International Conference on Computer Aided Verification
publication_identifier:
isbn:
- '9783540439974'
publication_status: published
publisher: Springer
publist_id: '146'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Synchronous and bidirectional component interfaces
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2404
year: '2002'
...
---
_id: '4563'
abstract:
- lang: eng
text: We present a formal methodology and tool for uncovering errors in the interaction
of software modules. Our methodology consists of a suite of languages for defining
software interfaces, and algorithms for checking interface compatibility. We focus
on interfaces that explain the method-call dependencies between software modules.
Such an interface makes assumptions about the environment in the form of call
and availability constraints. A call constraint restricts the accessibility of
local methods to certain external methods. An availability constraint restricts
the accessibility of local methods to certain states of the module. For example,
the interface for a file server with local methods open and read may assert that
a file cannot be read without having been opened. Checking interface compatibility
requires the solution of games, and in the presence of availability constraints,
of pushdown games. Based on this methodology, we have implemented a tool that
has uncovered incompatibilities in TinyOS, a small operating system for sensor
nodes in adhoc networks.
acknowledgement: This research was supported in part by the AFOSR grant F49620-00-1-0327,
the DARPA grant F33615-00-C-1693, the MARCO grant 98-DT-660, the NSF grants CCR-9988172,
CCR-0085949, CCR-0132780, the SRC grant 99-TJ-683, and the Polish KBN grant 7-T11C-027-20.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Arindam
full_name: Chakrabarti, Arindam
last_name: Chakrabarti
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Marcin
full_name: Jurdziński, Marcin
last_name: Jurdziński
- first_name: Freddy
full_name: Mang, Freddy
last_name: Mang
citation:
ama: 'Chakrabarti A, De Alfaro L, Henzinger TA, Jurdziński M, Mang F. Interface
compatibility checking for software modules. In: Proceedings of the 14th International
Conference on Computer Aided Verification. Vol 2404. Springer; 2002:428-441.
doi:10.1007/3-540-45657-0_35'
apa: 'Chakrabarti, A., De Alfaro, L., Henzinger, T. A., Jurdziński, M., & Mang,
F. (2002). Interface compatibility checking for software modules. In Proceedings
of the 14th International Conference on Computer Aided Verification (Vol.
2404, pp. 428–441). Copenhagen, Denmark: Springer. https://doi.org/10.1007/3-540-45657-0_35'
chicago: Chakrabarti, Arindam, Luca De Alfaro, Thomas A Henzinger, Marcin Jurdziński,
and Freddy Mang. “Interface Compatibility Checking for Software Modules.” In Proceedings
of the 14th International Conference on Computer Aided Verification, 2404:428–41.
Springer, 2002. https://doi.org/10.1007/3-540-45657-0_35.
ieee: A. Chakrabarti, L. De Alfaro, T. A. Henzinger, M. Jurdziński, and F. Mang,
“Interface compatibility checking for software modules,” in Proceedings of
the 14th International Conference on Computer Aided Verification, Copenhagen,
Denmark, 2002, vol. 2404, pp. 428–441.
ista: 'Chakrabarti A, De Alfaro L, Henzinger TA, Jurdziński M, Mang F. 2002. Interface
compatibility checking for software modules. Proceedings of the 14th International
Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS,
vol. 2404, 428–441.'
mla: Chakrabarti, Arindam, et al. “Interface Compatibility Checking for Software
Modules.” Proceedings of the 14th International Conference on Computer Aided
Verification, vol. 2404, Springer, 2002, pp. 428–41, doi:10.1007/3-540-45657-0_35.
short: A. Chakrabarti, L. De Alfaro, T.A. Henzinger, M. Jurdziński, F. Mang, in:,
Proceedings of the 14th International Conference on Computer Aided Verification,
Springer, 2002, pp. 428–441.
conference:
end_date: 2002-07-31
location: Copenhagen, Denmark
name: 'CAV: Computer Aided Verification'
start_date: 2002-07-27
date_created: 2018-12-11T12:09:30Z
date_published: 2002-06-19T00:00:00Z
date_updated: 2023-06-05T07:38:10Z
day: '19'
doi: 10.1007/3-540-45657-0_35
extern: '1'
intvolume: ' 2404'
language:
- iso: eng
month: '06'
oa_version: None
page: 428 - 441
publication: Proceedings of the 14th International Conference on Computer Aided Verification
publication_identifier:
isbn:
- ' 9783540439974'
publication_status: published
publisher: Springer
publist_id: '147'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Interface compatibility checking for software modules
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2404
year: '2002'
...
---
_id: '4565'
abstract:
- lang: eng
text: "In the literature, we find several formulations of the control\r\nproblem
for timed and hybrid systems. We argue that formulations where\r\na controller
can cause an action at any point in dense (rational or real)\r\ntime are problematic,
by presenting an example where the controller\r\nmust act faster and faster, yet
causes no Zeno effects (say, the control\r\nactions are at times 0, 1/2, 1, 1
1/4, 2, 2 1/8, 3, 3 1/16 ,...). Such a controller is,\r\nof course, not implementable
in software. Such controllers are avoided by formulations where the controller
can cause actions only at discrete (integer) points in time. While the resulting
control problem is well- understood if the time unit, or “sampling rate” of the
controller, is fixed a priori, we define a novel, stronger formulation: the discrete-time
control problem with unknown sampling rate asks if a sampling controller exists
for some sampling rate. We prove that this problem is undecidable even in the
special case of timed automata."
acknowledgement: "Partially supported by the FNRS, Belgium, under grant 1.5.096.01.\r\nPartially
supported by the DARPA SEC grant F33615-C-98-3614, the AFOSR MURI grant F49620-00-1-0327,
the NSF Theory grant CCR-9988172, and the MARCO GSRC grant 98-DT-660.\r\nPartially
supported by a “Crédit aux chercheurs” from the Belgian National Fund for Scientific
Research."
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Franck
full_name: Cassez, Franck
last_name: Cassez
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Jean
full_name: Raskin, Jean
last_name: Raskin
citation:
ama: 'Cassez F, Henzinger TA, Raskin J. A comparison of control problems for timed
and hybrid systems. In: Proceedings of the 5th International Workshop on Hybrid
Systems: Computation and Control. Vol 2289. Springer; 2002:134-148. doi:10.1007/3-540-45873-5_13'
apa: 'Cassez, F., Henzinger, T. A., & Raskin, J. (2002). A comparison of control
problems for timed and hybrid systems. In Proceedings of the 5th International
Workshop on Hybrid Systems: Computation and Control (Vol. 2289, pp. 134–148).
Stanford, CA, USA: Springer. https://doi.org/10.1007/3-540-45873-5_13'
chicago: 'Cassez, Franck, Thomas A Henzinger, and Jean Raskin. “A Comparison of
Control Problems for Timed and Hybrid Systems.” In Proceedings of the 5th International
Workshop on Hybrid Systems: Computation and Control, 2289:134–48. Springer,
2002. https://doi.org/10.1007/3-540-45873-5_13.'
ieee: 'F. Cassez, T. A. Henzinger, and J. Raskin, “A comparison of control problems
for timed and hybrid systems,” in Proceedings of the 5th International Workshop
on Hybrid Systems: Computation and Control, Stanford, CA, USA, 2002, vol.
2289, pp. 134–148.'
ista: 'Cassez F, Henzinger TA, Raskin J. 2002. A comparison of control problems
for timed and hybrid systems. Proceedings of the 5th International Workshop on
Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and
Control, LNCS, vol. 2289, 134–148.'
mla: 'Cassez, Franck, et al. “A Comparison of Control Problems for Timed and Hybrid
Systems.” Proceedings of the 5th International Workshop on Hybrid Systems:
Computation and Control, vol. 2289, Springer, 2002, pp. 134–48, doi:10.1007/3-540-45873-5_13.'
short: 'F. Cassez, T.A. Henzinger, J. Raskin, in:, Proceedings of the 5th International
Workshop on Hybrid Systems: Computation and Control, Springer, 2002, pp. 134–148.'
conference:
end_date: 2002-03-27
location: Stanford, CA, USA
name: 'HSCC: Hybrid Systems - Computation and Control'
start_date: 2002-03-25
date_created: 2018-12-11T12:09:30Z
date_published: 2002-03-14T00:00:00Z
date_updated: 2023-06-02T10:29:10Z
day: '14'
doi: 10.1007/3-540-45873-5_13
extern: '1'
intvolume: ' 2289'
language:
- iso: eng
month: '03'
oa_version: None
page: 134 - 148
publication: 'Proceedings of the 5th International Workshop on Hybrid Systems: Computation
and Control'
publication_identifier:
isbn:
- '9783540433217'
publication_status: published
publisher: Springer
publist_id: '144'
quality_controlled: '1'
scopus_import: '1'
status: public
title: A comparison of control problems for timed and hybrid systems
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2289
year: '2002'
...
---
_id: '4595'
abstract:
- lang: eng
text: 'Temporal logic comes in two varieties: linear-time temporal logic assumes
implicit universal quantification over all paths that are generated by the execution
of a system; branching-time temporal logic allows explicit existential and universal
quantification over all paths. We introduce a third, more general variety of temporal
logic: alternating-time temporal logic offers selective quantification over those
paths that are possible outcomes of games, such as the game in which the system
and the environment alternate moves. While linear-time and branching-time logics
are natural specification languages for closed systems, alternating-time logics
are natural specification languages for open systems. For example, by preceding
the temporal operator "eventually" with a selective path quantifier,
we can specify that in the game between the system and the environment, the system
has a strategy to reach a certain state. The problems of receptiveness, realizability,
and controllability can be formulated as model-checking problems for alternating-time
formulas. Depending on whether or not we admit arbitrary nesting of selective
path quantifiers and temporal operators, we obtain the two alternating-time temporal
logics ATL and ATL*.ATL and ATL* are interpreted over concurrent game structures.
Every state transition of a concurrent game structure results from a choice of
moves, one for each player. The players represent individual components and the
environment of an open system. Concurrent game structures can capture various
forms of synchronous composition for open systems, and if augmented with fairness
constraints, also asynchronous composition. Over structures without fairness constraints,
the model-checking complexity of ATL is linear in the size of the game structure
and length of the formula, and the symbolic model-checking algorithm for CTL extends
with few modifications to ATL. Over structures with weak-fairness constraints,
ATL model checking requires the solution of 1-pair Rabin games, and can be done
in polynomial time. Over structures with strong-fairness constraints, ATL model
checking requires the solution of games with Boolean combinations of Büchi conditions,
and can be done in PSPACE. In the case of ATL*, the model-checking problem is
closely related to the synthesis problem for linear-time formulas, and requires
doubly exponential time.'
acknowledgement: We thank Luca de Alfaro, Kousha Etessami, Salvatore La Torre, P.
Madhusudan, Amir Pnueli, Moshe Vardi, Thomas Wilke, and Mihalis Yannakakis for helpful
discussions. We also thank Freddy Mang for comments on a draft of this manuscript.
article_processing_charge: No
article_type: original
author:
- first_name: Rajeev
full_name: Alur, Rajeev
last_name: Alur
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Orna
full_name: Kupferman, Orna
last_name: Kupferman
citation:
ama: Alur R, Henzinger TA, Kupferman O. Alternating-time temporal logic. Journal
of the ACM. 2002;49(5):672-713. doi:10.1145/585265.585270
apa: Alur, R., Henzinger, T. A., & Kupferman, O. (2002). Alternating-time temporal
logic. Journal of the ACM. ACM. https://doi.org/10.1145/585265.585270
chicago: Alur, Rajeev, Thomas A Henzinger, and Orna Kupferman. “Alternating-Time
Temporal Logic.” Journal of the ACM. ACM, 2002. https://doi.org/10.1145/585265.585270.
ieee: R. Alur, T. A. Henzinger, and O. Kupferman, “Alternating-time temporal logic,”
Journal of the ACM, vol. 49, no. 5. ACM, pp. 672–713, 2002.
ista: Alur R, Henzinger TA, Kupferman O. 2002. Alternating-time temporal logic.
Journal of the ACM. 49(5), 672–713.
mla: Alur, Rajeev, et al. “Alternating-Time Temporal Logic.” Journal of the ACM,
vol. 49, no. 5, ACM, 2002, pp. 672–713, doi:10.1145/585265.585270.
short: R. Alur, T.A. Henzinger, O. Kupferman, Journal of the ACM 49 (2002) 672–713.
date_created: 2018-12-11T12:09:40Z
date_published: 2002-09-01T00:00:00Z
date_updated: 2023-06-02T10:07:22Z
day: '01'
doi: 10.1145/585265.585270
extern: '1'
intvolume: ' 49'
issue: '5'
language:
- iso: eng
month: '09'
oa_version: None
page: 672 - 713
publication: Journal of the ACM
publication_identifier:
issn:
- 0004-5411
publication_status: published
publisher: ACM
publist_id: '110'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Alternating-time temporal logic
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 49
year: '2002'
...
---
_id: '4631'
abstract:
- lang: eng
text: We present a theory of timed interfaces, which is capable of specifying both
the timing of the inputs a component expects from the environment, and the timing
of the outputs it can produce. Two timed interfaces are compatible if there is
a way to use them together such that their timing expectations are met. Our theory
provides algorithms for checking the compatibility between two interfaces and
for deriving the composite interface; the theory can thus be viewed as a type
system for real-time interaction. Technically, a timed interface is encoded as
a timed game between two players, representing the inputs and outputs of the component.
The algorithms for compatibility checking and interface composition are thus derived
from algorithms for solving timed games.
acknowledgement: This research was supported in part by the NSF CAREER award CCR-0132780,
the NSF grant CCR-9988172 the AFOSR MURI grant F49620-00-1-0327, the DARPA PCES
grant F33615-00-C-1693, the MARCO GSRC grant 98-DT-660, and the ONR grant N00014-02-1-0671.
alternative_title:
- LNCS
article_processing_charge: No
author:
- first_name: Luca
full_name: De Alfaro, Luca
last_name: De Alfaro
- first_name: Thomas A
full_name: Henzinger, Thomas A
id: 40876CD8-F248-11E8-B48F-1D18A9856A87
last_name: Henzinger
orcid: 0000−0002−2985−7724
- first_name: Mariëlle
full_name: Stoelinga, Mariëlle
last_name: Stoelinga
citation:
ama: 'De Alfaro L, Henzinger TA, Stoelinga M. Timed interfaces. In: Proceedings
of the 2nd International Conference on Embedded Software. Vol 2491. ACM; 2002:108-122.
doi:10.1007/3-540-45828-X_9'
apa: 'De Alfaro, L., Henzinger, T. A., & Stoelinga, M. (2002). Timed interfaces.
In Proceedings of the 2nd International Conference on Embedded Software
(Vol. 2491, pp. 108–122). Grenoble, France: ACM. https://doi.org/10.1007/3-540-45828-X_9'
chicago: De Alfaro, Luca, Thomas A Henzinger, and Mariëlle Stoelinga. “Timed Interfaces.”
In Proceedings of the 2nd International Conference on Embedded Software,
2491:108–22. ACM, 2002. https://doi.org/10.1007/3-540-45828-X_9.
ieee: L. De Alfaro, T. A. Henzinger, and M. Stoelinga, “Timed interfaces,” in Proceedings
of the 2nd International Conference on Embedded Software, Grenoble, France,
2002, vol. 2491, pp. 108–122.
ista: 'De Alfaro L, Henzinger TA, Stoelinga M. 2002. Timed interfaces. Proceedings
of the 2nd International Conference on Embedded Software. EMSOFT: Embedded Software
, LNCS, vol. 2491, 108–122.'
mla: De Alfaro, Luca, et al. “Timed Interfaces.” Proceedings of the 2nd International
Conference on Embedded Software, vol. 2491, ACM, 2002, pp. 108–22, doi:10.1007/3-540-45828-X_9.
short: L. De Alfaro, T.A. Henzinger, M. Stoelinga, in:, Proceedings of the 2nd International
Conference on Embedded Software, ACM, 2002, pp. 108–122.
conference:
end_date: 2002-10-09
location: Grenoble, France
name: 'EMSOFT: Embedded Software '
start_date: 2002-10-07
date_created: 2018-12-11T12:09:51Z
date_published: 2002-10-24T00:00:00Z
date_updated: 2023-06-02T10:00:32Z
day: '24'
doi: 10.1007/3-540-45828-X_9
extern: '1'
intvolume: ' 2491'
language:
- iso: eng
month: '10'
oa_version: None
page: 108 - 122
publication: Proceedings of the 2nd International Conference on Embedded Software
publication_identifier:
isbn:
- '9783540443070'
publication_status: published
publisher: ACM
publist_id: '76'
quality_controlled: '1'
status: public
title: Timed interfaces
type: conference
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2491
year: '2002'
...
---
_id: '841'
article_processing_charge: No
article_type: original
author:
- first_name: Yuri
full_name: Wolf, Yuri
last_name: Wolf
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
citation:
ama: 'Wolf Y, Kondrashov F, Koonin E. Footprints of primordial introns on the eukaryotic
genome: still no clear traces . Trends in Genetics. 2001;17(9):499-501.
doi:10.1016/S0168-9525(01)02376-9'
apa: 'Wolf, Y., Kondrashov, F., & Koonin, E. (2001). Footprints of primordial
introns on the eukaryotic genome: still no clear traces . Trends in Genetics.
Elsevier. https://doi.org/10.1016/S0168-9525(01)02376-9'
chicago: 'Wolf, Yuri, Fyodor Kondrashov, and Eugene Koonin. “Footprints of Primordial
Introns on the Eukaryotic Genome: Still No Clear Traces .” Trends in Genetics.
Elsevier, 2001. https://doi.org/10.1016/S0168-9525(01)02376-9.'
ieee: 'Y. Wolf, F. Kondrashov, and E. Koonin, “Footprints of primordial introns
on the eukaryotic genome: still no clear traces ,” Trends in Genetics,
vol. 17, no. 9. Elsevier, pp. 499–501, 2001.'
ista: 'Wolf Y, Kondrashov F, Koonin E. 2001. Footprints of primordial introns on
the eukaryotic genome: still no clear traces . Trends in Genetics. 17(9), 499–501.'
mla: 'Wolf, Yuri, et al. “Footprints of Primordial Introns on the Eukaryotic Genome:
Still No Clear Traces .” Trends in Genetics, vol. 17, no. 9, Elsevier,
2001, pp. 499–501, doi:10.1016/S0168-9525(01)02376-9.'
short: Y. Wolf, F. Kondrashov, E. Koonin, Trends in Genetics 17 (2001) 499–501.
date_created: 2018-12-11T11:48:47Z
date_published: 2001-09-01T00:00:00Z
date_updated: 2023-06-02T09:38:37Z
day: '01'
doi: 10.1016/S0168-9525(01)02376-9
extern: '1'
external_id:
pmid:
- '11721681'
intvolume: ' 17'
issue: '9'
language:
- iso: eng
month: '09'
oa_version: None
page: 499 - 501
pmid: 1
publication: Trends in Genetics
publication_identifier:
issn:
- 0168-9479
publication_status: published
publisher: Elsevier
publist_id: '6805'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Footprints of primordial introns on the eukaryotic genome: still no clear
traces '
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 17
year: '2001'
...
---
_id: '851'
abstract:
- lang: eng
text: 'The study and comparison of mutation(al) spectra is an important problem
in molecular biology, because these spectra often reflect on important features
of mutations and their fixation. Such features include the interaction of DNA
with various mutagens, the function of repair/replication enzymes, and properties
of target proteins. It is known that mutability varies significantly along nucleotide
sequences, such that mutations often concentrate at certain positions, called
"hotspots," in a sequence. In this paper, we discuss in detail two approaches
for mutation spectra analysis: the comparison of mutation spectra with a HG-PUBL
program, (FTP: sunsite.unc.edu/pub/academic/ biology/dna-mutations/hyperg) and
hotspot prediction with the CLUSTERM program (www.itba.mi.cnr.it/webmutation;
ftp.bionet.nsc.ru/pub/biology/dbms/clusterm.zip). Several other approaches for
mutational spectra analysis, such as the analysis of a target protein structure,
hotspot context revealing, multiple spectra comparisons, as well as a number of
mutation databases are briefly described. Mutation spectra in the lacI gene of
E. coli and the human p53 gene are used for illustration of various difficulties
of such analysis.'
acknowledgement: 'Russian Fund of Fundamental Research. Grant Number: 99-04-49535.
NIH. Grant Number: GM 20293. NASA. Grant Number: NCC2-1057'
article_processing_charge: No
article_type: original
author:
- first_name: Igor
full_name: Rogozin, Igor
last_name: Rogozin
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Galina
full_name: Glazko, Galina
last_name: Glazko
citation:
ama: Rogozin I, Kondrashov F, Glazko G. Use of mutation spectra analysis software.
Human Mutation. 2001;17(2):83-102. doi:10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E
apa: Rogozin, I., Kondrashov, F., & Glazko, G. (2001). Use of mutation spectra
analysis software. Human Mutation. Wiley-Blackwell. https://doi.org/10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E
chicago: Rogozin, Igor, Fyodor Kondrashov, and Galina Glazko. “Use of Mutation Spectra
Analysis Software.” Human Mutation. Wiley-Blackwell, 2001. https://doi.org/10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E.
ieee: I. Rogozin, F. Kondrashov, and G. Glazko, “Use of mutation spectra analysis
software,” Human Mutation, vol. 17, no. 2. Wiley-Blackwell, pp. 83–102,
2001.
ista: Rogozin I, Kondrashov F, Glazko G. 2001. Use of mutation spectra analysis
software. Human Mutation. 17(2), 83–102.
mla: Rogozin, Igor, et al. “Use of Mutation Spectra Analysis Software.” Human
Mutation, vol. 17, no. 2, Wiley-Blackwell, 2001, pp. 83–102, doi:10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E.
short: I. Rogozin, F. Kondrashov, G. Glazko, Human Mutation 17 (2001) 83–102.
date_created: 2018-12-11T11:48:50Z
date_published: 2001-01-01T00:00:00Z
date_updated: 2023-06-02T09:22:17Z
day: '01'
doi: 10.1002/1098-1004(200102)17:2<83::AID-HUMU1>3.0.CO;2-E
extern: '1'
external_id:
pmid:
- '11180592'
intvolume: ' 17'
issue: '2'
language:
- iso: eng
month: '01'
oa_version: None
page: 83 - 102
pmid: 1
publication: Human Mutation
publication_identifier:
issn:
- 1059-7794
publication_status: published
publisher: Wiley-Blackwell
publist_id: '6796'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Use of mutation spectra analysis software
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 17
year: '2001'
...
---
_id: '8521'
abstract:
- lang: eng
text: We continue the previous article's discussion of bounds, for prevalent diffeomorphisms
of smooth compact manifolds, on the growth of the number of periodic points and
the decay of their hyperbolicity as a function of their period $n$. In that article
we reduced the main results to a problem, for certain families of diffeomorphisms,
of bounding the measure of parameter values for which the diffeomorphism has (for
a given period $n$) an almost periodic point that is almost nonhyperbolic. We
also formulated our results for $1$-dimensional endomorphisms on a compact interval.
In this article we describe some of the main techniques involved and outline the
rest of the proof. To simplify notation, we concentrate primarily on the $1$-dimensional
case.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Brian R.
full_name: Hunt, Brian R.
last_name: Hunt
citation:
ama: Kaloshin V, Hunt BR. A stretched exponential bound on the rate of growth of
the number of periodic points for prevalent diffeomorphisms II. Electronic
Research Announcements of the American Mathematical Society. 2001;7(5):28-36.
doi:10.1090/s1079-6762-01-00091-9
apa: Kaloshin, V., & Hunt, B. R. (2001). A stretched exponential bound on the
rate of growth of the number of periodic points for prevalent diffeomorphisms
II. Electronic Research Announcements of the American Mathematical Society.
American Mathematical Society. https://doi.org/10.1090/s1079-6762-01-00091-9
chicago: Kaloshin, Vadim, and Brian R. Hunt. “A Stretched Exponential Bound on the
Rate of Growth of the Number of Periodic Points for Prevalent Diffeomorphisms
II.” Electronic Research Announcements of the American Mathematical Society.
American Mathematical Society, 2001. https://doi.org/10.1090/s1079-6762-01-00091-9.
ieee: V. Kaloshin and B. R. Hunt, “A stretched exponential bound on the rate of
growth of the number of periodic points for prevalent diffeomorphisms II,” Electronic
Research Announcements of the American Mathematical Society, vol. 7, no. 5.
American Mathematical Society, pp. 28–36, 2001.
ista: Kaloshin V, Hunt BR. 2001. A stretched exponential bound on the rate of growth
of the number of periodic points for prevalent diffeomorphisms II. Electronic
Research Announcements of the American Mathematical Society. 7(5), 28–36.
mla: Kaloshin, Vadim, and Brian R. Hunt. “A Stretched Exponential Bound on the Rate
of Growth of the Number of Periodic Points for Prevalent Diffeomorphisms II.”
Electronic Research Announcements of the American Mathematical Society,
vol. 7, no. 5, American Mathematical Society, 2001, pp. 28–36, doi:10.1090/s1079-6762-01-00091-9.
short: V. Kaloshin, B.R. Hunt, Electronic Research Announcements of the American
Mathematical Society 7 (2001) 28–36.
date_created: 2020-09-18T10:49:43Z
date_published: 2001-04-24T00:00:00Z
date_updated: 2021-01-12T08:19:51Z
day: '24'
doi: 10.1090/s1079-6762-01-00091-9
extern: '1'
intvolume: ' 7'
issue: '5'
keyword:
- General Mathematics
language:
- iso: eng
month: '04'
oa_version: None
page: 28-36
publication: Electronic Research Announcements of the American Mathematical Society
publication_identifier:
issn:
- 1079-6762
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: A stretched exponential bound on the rate of growth of the number of periodic
points for prevalent diffeomorphisms II
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2001'
...
---
_id: '8522'
abstract:
- lang: eng
text: For diffeomorphisms of smooth compact manifolds, we consider the problem of
how fast the number of periodic points with period $n$grows as a function of $n$.
In many familiar cases (e.g., Anosov systems) the growth is exponential, but arbitrarily
fast growth is possible; in fact, the first author has shown that arbitrarily
fast growth is topologically (Baire) generic for $C^2$ or smoother diffeomorphisms.
In the present work we show that, by contrast, for a measure-theoretic notion
of genericity we call ``prevalence'', the growth is not much faster than exponential.
Specifically, we show that for each $\delta > 0$, there is a prevalent set of
( $C^{1+\rho}$ or smoother) diffeomorphisms for which the number of period $n$
points is bounded above by $\operatorname{exp}(C n^{1+\delta})$ for some $C$ independent
of $n$. We also obtain a related bound on the decay of the hyperbolicity of the
periodic points as a function of $n$. The contrast between topologically generic
and measure-theoretically generic behavior for the growth of the number of periodic
points and the decay of their hyperbolicity shows this to be a subtle and complex
phenomenon, reminiscent of KAM theory.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Brian R.
full_name: Hunt, Brian R.
last_name: Hunt
citation:
ama: Kaloshin V, Hunt BR. A stretched exponential bound on the rate of growth of
the number of periodic points for prevalent diffeomorphisms I. Electronic Research
Announcements of the American Mathematical Society. 2001;7(4):17-27. doi:10.1090/s1079-6762-01-00090-7
apa: Kaloshin, V., & Hunt, B. R. (2001). A stretched exponential bound on the
rate of growth of the number of periodic points for prevalent diffeomorphisms
I. Electronic Research Announcements of the American Mathematical Society.
American Mathematical Society. https://doi.org/10.1090/s1079-6762-01-00090-7
chicago: Kaloshin, Vadim, and Brian R. Hunt. “A Stretched Exponential Bound on the
Rate of Growth of the Number of Periodic Points for Prevalent Diffeomorphisms
I.” Electronic Research Announcements of the American Mathematical Society.
American Mathematical Society, 2001. https://doi.org/10.1090/s1079-6762-01-00090-7.
ieee: V. Kaloshin and B. R. Hunt, “A stretched exponential bound on the rate of
growth of the number of periodic points for prevalent diffeomorphisms I,” Electronic
Research Announcements of the American Mathematical Society, vol. 7, no. 4.
American Mathematical Society, pp. 17–27, 2001.
ista: Kaloshin V, Hunt BR. 2001. A stretched exponential bound on the rate of growth
of the number of periodic points for prevalent diffeomorphisms I. Electronic Research
Announcements of the American Mathematical Society. 7(4), 17–27.
mla: Kaloshin, Vadim, and Brian R. Hunt. “A Stretched Exponential Bound on the Rate
of Growth of the Number of Periodic Points for Prevalent Diffeomorphisms I.” Electronic
Research Announcements of the American Mathematical Society, vol. 7, no. 4,
American Mathematical Society, 2001, pp. 17–27, doi:10.1090/s1079-6762-01-00090-7.
short: V. Kaloshin, B.R. Hunt, Electronic Research Announcements of the American
Mathematical Society 7 (2001) 17–27.
date_created: 2020-09-18T10:49:56Z
date_published: 2001-04-18T00:00:00Z
date_updated: 2021-01-12T08:19:51Z
day: '18'
doi: 10.1090/s1079-6762-01-00090-7
extern: '1'
intvolume: ' 7'
issue: '4'
keyword:
- General Mathematics
language:
- iso: eng
month: '04'
oa_version: None
page: 17-27
publication: Electronic Research Announcements of the American Mathematical Society
publication_identifier:
issn:
- 1079-6762
publication_status: published
publisher: American Mathematical Society
quality_controlled: '1'
status: public
title: A stretched exponential bound on the rate of growth of the number of periodic
points for prevalent diffeomorphisms I
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 7
year: '2001'
...
---
_id: '8524'
abstract:
- lang: eng
text: 'A number α∈R is diophantine if it is not well approximable by rationals,
i.e. for some C,ε>0 and any relatively prime p,q∈Z we have |αq−p|>Cq−1−ε. It is
well-known and is easy to prove that almost every α in R is diophantine. In this
paper we address a noncommutative version of the diophantine properties. Consider
a pair A,B∈SO(3) and for each n∈Z+ take all possible words in A, A -1, B, and
B - 1 of length n, i.e. for a multiindex I=(i1,i1,…,im,jm) define |I|=∑mk=1(|ik|+|jk|)=n
and \( W_n(A,B ) = \{W_{\cal I}(A,B) = A^{i_1} B^{j_1} \dots A^{i_m} B^{j_m}\}_{|{\cal
I|}=n \).¶Gamburd—Jakobson—Sarnak [GJS] raised the problem: prove that for Haar
almost every pair A,B∈SO(3) the closest distance of words of length n to the identity,
i.e. sA,B(n)=min|I|=n∥WI(A,B)−E∥, is bounded from below by an exponential function
in n. This is the analog of the diophantine property for elements of SO(3). In
this paper we prove that s A,B (n) is bounded from below by an exponential function
in n 2. We also exhibit obstructions to a “simple” proof of the exponential estimate
in n.'
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: I.
full_name: Rodnianski, I.
last_name: Rodnianski
citation:
ama: Kaloshin V, Rodnianski I. Diophantine properties of elements of SO(3). Geometric
And Functional Analysis. 2001;11(5):953-970. doi:10.1007/s00039-001-8222-8
apa: Kaloshin, V., & Rodnianski, I. (2001). Diophantine properties of elements
of SO(3). Geometric And Functional Analysis. Springer Nature. https://doi.org/10.1007/s00039-001-8222-8
chicago: Kaloshin, Vadim, and I. Rodnianski. “Diophantine Properties of Elements
of SO(3).” Geometric And Functional Analysis. Springer Nature, 2001. https://doi.org/10.1007/s00039-001-8222-8.
ieee: V. Kaloshin and I. Rodnianski, “Diophantine properties of elements of SO(3),”
Geometric And Functional Analysis, vol. 11, no. 5. Springer Nature, pp.
953–970, 2001.
ista: Kaloshin V, Rodnianski I. 2001. Diophantine properties of elements of SO(3).
Geometric And Functional Analysis. 11(5), 953–970.
mla: Kaloshin, Vadim, and I. Rodnianski. “Diophantine Properties of Elements of
SO(3).” Geometric And Functional Analysis, vol. 11, no. 5, Springer Nature,
2001, pp. 953–70, doi:10.1007/s00039-001-8222-8.
short: V. Kaloshin, I. Rodnianski, Geometric And Functional Analysis 11 (2001) 953–970.
date_created: 2020-09-18T10:50:11Z
date_published: 2001-12-01T00:00:00Z
date_updated: 2021-01-12T08:19:52Z
day: '01'
doi: 10.1007/s00039-001-8222-8
extern: '1'
intvolume: ' 11'
issue: '5'
language:
- iso: eng
month: '12'
oa_version: None
page: 953-970
publication: Geometric And Functional Analysis
publication_identifier:
issn:
- 1016-443X
- 1420-8970
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Diophantine properties of elements of SO(3)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2001'
...
---
_id: '855'
abstract:
- lang: eng
text: 'Motivation: The context of the start codon (typically, AUG) and the features
of the 5′ Untranslated Regions (5′ UTRs) are important for understanding translation
regulation in eukaryotic mRNAs and for accurate prediction of the coding region
in genomic and cDNA sequences. The presence of AUG triplets in 5′ UTRs (upstream
AUGs) might effect the initiation rate and, in the context of gene prediction,
could reduce the accuracy of the identification of the authentic start. To reveal
potential connections between the presence of upstream AUGs and other features
of 5′ UTRs, such as their length and the start codon context, we undertook a systematic
analysis of the available eukaryotic 5′ UTR sequences. Results: We show that a
large fraction of 5′ UTRs in the available cDNA sequences, 15-53% depending on
the organism, contain upstream ATGs. A negative correlation was observed between
the information content of the translation start signal and the length of the
5′ UTR. Similarly, a negative correlation exists between the ''strength'' of the
start context and the number of upstream ATGs. Typically, cDNAs containing long
5′ UTRs with multiple upstream ATGs have a ''weak'' start context, and in contrast,
cDNAs containing short 5′ UTRs without ATGs have ''strong'' starts. These counter-intuitive
results may be interpreted in terms of upstream AUGs having an important role
in the regulation of translation efficiency by ensuring low basal translation
level via double negative control and creating the potential for additional regulatory
mechanisms. One of such mechanisms, supported by experimental studies of some
mRNAs, includes removal of the AUG-containing portion of the 5′ UTR by alternative
splicing.'
acknowledgement: This work has been partially supported by EU 'TRADAT' project and
by CNR Genetic Engineering (Italy), the RFBR grant for support of scientific schools
(00-15-97968) and SD RAS grant for young scientists (AVK). The authors wish to thank
J.Lyons-Weiler for helpful comments and A. Sorokin for help with the ATG_EVALUATOR
program.
article_processing_charge: No
article_type: original
author:
- first_name: Igor
full_name: Rogozin, Igor
last_name: Rogozin
- first_name: Alex
full_name: Kochetov, Alex
last_name: Kochetov
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
- first_name: Luciano
full_name: Milanesi, Luciano
last_name: Milanesi
citation:
ama: Rogozin I, Kochetov A, Kondrashov F, Koonin E, Milanesi L. Presence of ATG
triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with a ’weak’context
of the start codon. Bioinformatics. 2001;17(10):890-900. doi:10.1093/bioinformatics/17.10.890
apa: Rogozin, I., Kochetov, A., Kondrashov, F., Koonin, E., & Milanesi, L. (2001).
Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates
with a ’weak’context of the start codon. Bioinformatics. Oxford University
Press. https://doi.org/10.1093/bioinformatics/17.10.890
chicago: Rogozin, Igor, Alex Kochetov, Fyodor Kondrashov, Eugene Koonin, and Luciano
Milanesi. “Presence of ATG Triplets in 5′ Untranslated Regions of Eukaryotic CDNAs
Correlates with a ’weak’context of the Start Codon.” Bioinformatics. Oxford
University Press, 2001. https://doi.org/10.1093/bioinformatics/17.10.890.
ieee: I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, and L. Milanesi, “Presence
of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with
a ’weak’context of the start codon,” Bioinformatics, vol. 17, no. 10. Oxford
University Press, pp. 890–900, 2001.
ista: Rogozin I, Kochetov A, Kondrashov F, Koonin E, Milanesi L. 2001. Presence
of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates with
a ’weak’context of the start codon. Bioinformatics. 17(10), 890–900.
mla: Rogozin, Igor, et al. “Presence of ATG Triplets in 5′ Untranslated Regions
of Eukaryotic CDNAs Correlates with a ’weak’context of the Start Codon.” Bioinformatics,
vol. 17, no. 10, Oxford University Press, 2001, pp. 890–900, doi:10.1093/bioinformatics/17.10.890.
short: I. Rogozin, A. Kochetov, F. Kondrashov, E. Koonin, L. Milanesi, Bioinformatics
17 (2001) 890–900.
date_created: 2018-12-11T11:48:52Z
date_published: 2001-10-01T00:00:00Z
date_updated: 2023-06-02T09:08:25Z
day: '01'
doi: 10.1093/bioinformatics/17.10.890
extern: '1'
external_id:
pmid:
- '11673233'
intvolume: ' 17'
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
page: 890 - 900
pmid: 1
publication: Bioinformatics
publication_identifier:
issn:
- 1367-4803
publication_status: published
publisher: Oxford University Press
publist_id: '6795'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Presence of ATG triplets in 5′ untranslated regions of eukaryotic cDNAs correlates
with a 'weak'context of the start codon
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 17
year: '2001'
...
---
_id: '867'
abstract:
- lang: eng
text: Genes with new functions often evolve by gene duplication. Alternative splicing
is another means of evolutionary innovation in eukaryotes, which allows a single
gene to encode functionally diverse proteins. We investigate a connection between
these two evolutionary phenomena. For ∼10% of the described cases of substitution
alternative splicing, such that either one or another amino acid sequence is included
into the protein, evidence of origin by tandem exon duplication was found. This
is a conservative estimate because alternative exons are typically short and,
on many occasions, duplicates may have diverged beyond recognition. Dating exon
duplications through a combination of the available experimental data on alternative
splicing in orthologous genes from different species and computational analysis
indicates that most of the duplications antedate at least the radiation of mammalian
orders or even the radiation of vertebrate classes. At present, tandem exon duplication
is the only mechanism of evolution of substitution alternative splicing that can
be specifically demonstrated. Along with gene duplication, this could be a major
route for generating functional diversity during evolution of multicellular eukaryotes.
article_processing_charge: No
article_type: original
author:
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
citation:
ama: Kondrashov F, Koonin E. Origin of alternative splicing by tandem exon duplication.
Human Molecular Genetics. 2001;10(23):2661-2669. doi:10.1093/hmg/10.23.2661
apa: Kondrashov, F., & Koonin, E. (2001). Origin of alternative splicing by
tandem exon duplication. Human Molecular Genetics. Oxford University Press.
https://doi.org/10.1093/hmg/10.23.2661
chicago: Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing
by Tandem Exon Duplication.” Human Molecular Genetics. Oxford University
Press, 2001. https://doi.org/10.1093/hmg/10.23.2661.
ieee: F. Kondrashov and E. Koonin, “Origin of alternative splicing by tandem exon
duplication,” Human Molecular Genetics, vol. 10, no. 23. Oxford University
Press, pp. 2661–2669, 2001.
ista: Kondrashov F, Koonin E. 2001. Origin of alternative splicing by tandem exon
duplication. Human Molecular Genetics. 10(23), 2661–2669.
mla: Kondrashov, Fyodor, and Eugene Koonin. “Origin of Alternative Splicing by Tandem
Exon Duplication.” Human Molecular Genetics, vol. 10, no. 23, Oxford University
Press, 2001, pp. 2661–69, doi:10.1093/hmg/10.23.2661.
short: F. Kondrashov, E. Koonin, Human Molecular Genetics 10 (2001) 2661–2669.
date_created: 2018-12-11T11:48:55Z
date_published: 2001-11-01T00:00:00Z
date_updated: 2023-06-02T08:39:47Z
day: '01'
doi: 10.1093/hmg/10.23.2661
extern: '1'
external_id:
pmid:
- '11726553'
intvolume: ' 10'
issue: '23'
language:
- iso: eng
month: '11'
oa_version: Published Version
page: 2661 - 2669
pmid: 1
publication: Human Molecular Genetics
publication_identifier:
issn:
- 0964-6906
publication_status: published
publisher: Oxford University Press
publist_id: '6777'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Origin of alternative splicing by tandem exon duplication
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 10
year: '2001'
...
---
_id: '874'
abstract:
- lang: eng
text: Sex is thought to facilitate accumulation of initially rare beneficial mutations
by allowing simultaneous allele replacements at many loci. However, this advantage
of sex depends on a restrictive assumption that the fitness of a genotype is determined
by fitness potential, a single intermediate variable to which all loci contribute
additively, so that new alleles can accumulate in any order. Individual-based
simulations of sexual and asexual populations reveal that under generic selection,
sex often retards adaptive evolution. When new alleles are beneficial only if
they accumulate in a prescribed order, a sexual population may evolve two or more
times slower than an asexual population because only asexual reproduction allows
some overlap of successive allele replacements. Many other fitness surfaces lead
to an even greater disadvantage of sex. Thus, either sex exists in spite of its
impact on the rate of adaptive allele replacements, or natural fitness surfaces
have rather specific properties, at least at the scale of intrapopulation genetic
variability.
article_processing_charge: No
article_type: original
author:
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alexey
full_name: Kondrashov, Alexey
last_name: Kondrashov
citation:
ama: Kondrashov F, Kondrashov A. Multidimensional epistasis and the disadvantage
of sex. PNAS. 2001;98(21):12089-12092. doi:10.1073/pnas.211214298
apa: Kondrashov, F., & Kondrashov, A. (2001). Multidimensional epistasis and
the disadvantage of sex. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.211214298
chicago: Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis
and the Disadvantage of Sex.” PNAS. National Academy of Sciences, 2001.
https://doi.org/10.1073/pnas.211214298.
ieee: F. Kondrashov and A. Kondrashov, “Multidimensional epistasis and the disadvantage
of sex,” PNAS, vol. 98, no. 21. National Academy of Sciences, pp. 12089–12092,
2001.
ista: Kondrashov F, Kondrashov A. 2001. Multidimensional epistasis and the disadvantage
of sex. PNAS. 98(21), 12089–12092.
mla: Kondrashov, Fyodor, and Alexey Kondrashov. “Multidimensional Epistasis and
the Disadvantage of Sex.” PNAS, vol. 98, no. 21, National Academy of Sciences,
2001, pp. 12089–92, doi:10.1073/pnas.211214298.
short: F. Kondrashov, A. Kondrashov, PNAS 98 (2001) 12089–12092.
date_created: 2018-12-11T11:48:58Z
date_published: 2001-10-09T00:00:00Z
date_updated: 2023-06-02T08:18:22Z
day: '09'
doi: 10.1073/pnas.211214298
extern: '1'
external_id:
pmid:
- '11593020'
intvolume: ' 98'
issue: '21'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC59772/
month: '10'
oa: 1
oa_version: Published Version
page: 12089 - 12092
pmid: 1
publication: PNAS
publication_identifier:
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
publist_id: '6774'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Multidimensional epistasis and the disadvantage of sex
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 98
year: '2001'
...
---
_id: '888'
abstract:
- lang: eng
text: 'BACKGROUND: Detection of changes in a protein''s evolutionary rate may reveal
cases of change in that protein''s function. We developed and implemented a simple
relative rates test in an attempt to assess the rate constancy of protein evolution
and to detect cases of functional diversification between orthologous proteins.
The test was performed on clusters of orthologous protein sequences from complete
bacterial genomes (Chlamydia trachomatis, C. muridarum and Chlamydophila pneumoniae),
complete archaeal genomes (Pyrococcus horikoshii, P. abyssi and P. furiosus) and
partially sequenced mammalian genomes (human, mouse and rat). RESULTS: Amino-acid
sequence evolution rates are significantly correlated on different branches of
phylogenetic trees representing the great majority of analyzed orthologous protein
sets from all three domains of life. However, approximately 1% of the proteins
from each group of species deviates from this pattern and instead shows variation
that is consistent with an acceleration of the rate of amino-acid substitution,
which may be due to functional diversification. Most of the putative functionally
diversified proteins from all three species groups are predicted to function at
the periphery of the cells and mediate their interaction with the environment.
CONCLUSIONS: Relative rates of protein evolution are remarkably constant for the
three species groups analyzed here. Deviations from this rate constancy are probably
due to changes in selective constraints associated with diversification between
orthologs. Functional diversification between orthologs is thought to be a relatively
rare event. However, the resolution afforded by the test designed specifically
for genomic-scale datasets allowed us to identify numerous cases of possible functional
diversification between orthologous proteins.'
acknowledgement: We thank Alexey Kondrashov for many helpful discussions and constructive
criticisms, Charles DeLisi, David Landsman, Detlef Leipe, Wojciech Makalowski and
Itai Yanai for critical reading of the manuscript and constructive comments and
L. Aravind for advice on protein function prediction. The release of the unpublished
P. furiosus genome sequence by the Utah Genome Center at the University of Utah
is acknowledged and appreciated.
article_number: research0053.1
article_processing_charge: No
article_type: original
author:
- first_name: Ingo
full_name: Jordan, Ingo
last_name: Jordan
- first_name: Fyodor
full_name: Kondrashov, Fyodor
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Igor
full_name: Rogozin, Igor
last_name: Rogozin
- first_name: Roman
full_name: Tatusov, Roman
last_name: Tatusov
- first_name: Yuri
full_name: Wolf, Yuri
last_name: Wolf
- first_name: Eugene
full_name: Koonin, Eugene
last_name: Koonin
citation:
ama: Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. Constant relative
rate of protein evolution and detection of functional diversification among bacterial,
archaeal and eukaryotic proteins . Genome Biology. 2001;2(12). doi:10.1186/gb-2001-2-12-research0053
apa: Jordan, I., Kondrashov, F., Rogozin, I., Tatusov, R., Wolf, Y., & Koonin,
E. (2001). Constant relative rate of protein evolution and detection of functional
diversification among bacterial, archaeal and eukaryotic proteins . Genome
Biology. BioMed Central. https://doi.org/10.1186/gb-2001-2-12-research0053
chicago: Jordan, Ingo, Fyodor Kondrashov, Igor Rogozin, Roman Tatusov, Yuri Wolf,
and Eugene Koonin. “Constant Relative Rate of Protein Evolution and Detection
of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins
.” Genome Biology. BioMed Central, 2001. https://doi.org/10.1186/gb-2001-2-12-research0053.
ieee: I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, and E. Koonin,
“Constant relative rate of protein evolution and detection of functional diversification
among bacterial, archaeal and eukaryotic proteins ,” Genome Biology, vol.
2, no. 12. BioMed Central, 2001.
ista: Jordan I, Kondrashov F, Rogozin I, Tatusov R, Wolf Y, Koonin E. 2001. Constant
relative rate of protein evolution and detection of functional diversification
among bacterial, archaeal and eukaryotic proteins . Genome Biology. 2(12), research0053.1.
mla: Jordan, Ingo, et al. “Constant Relative Rate of Protein Evolution and Detection
of Functional Diversification among Bacterial, Archaeal and Eukaryotic Proteins
.” Genome Biology, vol. 2, no. 12, research0053.1, BioMed Central, 2001,
doi:10.1186/gb-2001-2-12-research0053.
short: I. Jordan, F. Kondrashov, I. Rogozin, R. Tatusov, Y. Wolf, E. Koonin, Genome
Biology 2 (2001).
date_created: 2018-12-11T11:49:02Z
date_published: 2001-01-01T00:00:00Z
date_updated: 2023-05-31T12:15:37Z
day: '01'
doi: 10.1186/gb-2001-2-12-research0053
extern: '1'
external_id:
pmid:
- '11790256'
intvolume: ' 2'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC64838/
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
issn:
- 1465-6906
publication_status: published
publisher: BioMed Central
publist_id: '6758'
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Constant relative rate of protein evolution and detection of functional diversification
among bacterial, archaeal and eukaryotic proteins '
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 2
year: '2001'
...
---
_id: '1452'
abstract:
- lang: eng
text: 'In this Note we present pairs of hyperkähler orbifolds which satisfy two
different versions of mirror symmetry. On the one hand, we show that their Hodge
numbers (or more precisely, stringy E-polynomials) are equal. On the other hand,
we show that they satisfy the prescription of Strominger, Yau, and Zaslow (which
in the present case goes back to Bershadsky, Johansen, Sadov and Vafa): that a
Calabi-Yau and its mirror should fiber over the same real manifold, with special
Lagrangian fibers which are tori dual to each other. Our examples arise as moduli
spaces of local systems on a curve with structure group SL(n); the mirror is the
corresponding space with structure group PGL(n). The special Lagrangian tori come
from an algebraically completely integrable Hamiltonian system: the Hitchin system.'
acknowledgement: The authors are grateful for Nigel Hitchin for suggesting the similarity
between [4] and [12] in 1996 and for Pierre Deligne for numerous useful comments
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Tamas
full_name: Hausel, Tamas
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
- first_name: Michael
full_name: Thaddeus, Michael
last_name: Thaddeus
citation:
ama: 'Hausel T, Thaddeus M. Examples of mirror partners arising from integrable
systems. Comptes Rendus de l’Academie des Sciences - Series I: Mathematics.
2001;333(4):313-318. doi:10.1016/S0764-4442(01)02057-2'
apa: 'Hausel, T., & Thaddeus, M. (2001). Examples of mirror partners arising
from integrable systems. Comptes Rendus de l’Academie Des Sciences - Series
I: Mathematics. Elsevier. https://doi.org/10.1016/S0764-4442(01)02057-2'
chicago: 'Hausel, Tamás, and Michael Thaddeus. “Examples of Mirror Partners Arising
from Integrable Systems.” Comptes Rendus de l’Academie Des Sciences - Series
I: Mathematics. Elsevier, 2001. https://doi.org/10.1016/S0764-4442(01)02057-2.'
ieee: 'T. Hausel and M. Thaddeus, “Examples of mirror partners arising from integrable
systems,” Comptes Rendus de l’Academie des Sciences - Series I: Mathematics,
vol. 333, no. 4. Elsevier, pp. 313–318, 2001.'
ista: 'Hausel T, Thaddeus M. 2001. Examples of mirror partners arising from integrable
systems. Comptes Rendus de l’Academie des Sciences - Series I: Mathematics. 333(4),
313–318.'
mla: 'Hausel, Tamás, and Michael Thaddeus. “Examples of Mirror Partners Arising
from Integrable Systems.” Comptes Rendus de l’Academie Des Sciences - Series
I: Mathematics, vol. 333, no. 4, Elsevier, 2001, pp. 313–18, doi:10.1016/S0764-4442(01)02057-2.'
short: 'T. Hausel, M. Thaddeus, Comptes Rendus de l’Academie Des Sciences - Series
I: Mathematics 333 (2001) 313–318.'
date_created: 2018-12-11T11:52:06Z
date_published: 2001-08-15T00:00:00Z
date_updated: 2023-05-31T09:57:48Z
day: '15'
doi: 10.1016/S0764-4442(01)02057-2
extern: '1'
external_id:
arxiv:
- math/0106140
intvolume: ' 333'
issue: '4'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/math/0106140
month: '08'
oa: 1
oa_version: Preprint
page: 313 - 318
publication: 'Comptes Rendus de l''Academie des Sciences - Series I: Mathematics'
publication_identifier:
issn:
- 0764-4442
publication_status: published
publisher: Elsevier
publist_id: '5742'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Examples of mirror partners arising from integrable systems
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 333
year: '2001'
...
---
_id: '1453'
abstract:
- lang: eng
text: In this Letter we exhibit a one-parameter family of new Taub-NUT instantons
parameterized by a half-line. The endpoint of the half-line will be the reducible
Yang-Mills instanton corresponding to the Eguchi-Hanson-Gibbons L2 harmonic 2-form,
while at an inner point we recover the Pope-Yuille instanton constructed as a
projection of the Levi-Civitá connection onto the positive su(2)+ ⊂ so(4) subalgebra.
Our method imitates the Jackiw-Nohl-Rebbi construction originally designed for
flat R4. That is we find a one-parameter family of harmonic functions on the Taub-NUT
space with a point singularity, rescale the metric and project the obtained Levi-Civitá
connection onto the other negative su(2)- ⊂ so(4) part. Our solutions will possess
the full U(2) symmetry, and thus provide more solutions to the recently proposed
U(2) symmetric ansatz of Kim and Yoon.
acknowledgement: We would like to acknowledge the financial support provided by the
Miller Institute of Basic Research in Science, the Japan Society for the Promotion
of Science, grant No. P99736 and the partial support by OTKA grant No. T032478.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Gábor
full_name: Etesi, Gábor
last_name: Etesi
- first_name: Tamas
full_name: Hausel, Tamas
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
citation:
ama: 'Etesi G, Hausel T. Geometric construction of new Yang-Mills instantons over
Taub-NUT space. Physics Letters, Section B: Nuclear, Elementary Particle and
High-Energy Physics. 2001;514(1-2):189-199. doi:10.1016/S0370-2693(01)00821-8'
apa: 'Etesi, G., & Hausel, T. (2001). Geometric construction of new Yang-Mills
instantons over Taub-NUT space. Physics Letters, Section B: Nuclear, Elementary
Particle and High-Energy Physics. Elsevier. https://doi.org/10.1016/S0370-2693(01)00821-8'
chicago: 'Etesi, Gábor, and Tamás Hausel. “Geometric Construction of New Yang-Mills
Instantons over Taub-NUT Space.” Physics Letters, Section B: Nuclear, Elementary
Particle and High-Energy Physics. Elsevier, 2001. https://doi.org/10.1016/S0370-2693(01)00821-8.'
ieee: 'G. Etesi and T. Hausel, “Geometric construction of new Yang-Mills instantons
over Taub-NUT space,” Physics Letters, Section B: Nuclear, Elementary Particle
and High-Energy Physics, vol. 514, no. 1–2. Elsevier, pp. 189–199, 2001.'
ista: 'Etesi G, Hausel T. 2001. Geometric construction of new Yang-Mills instantons
over Taub-NUT space. Physics Letters, Section B: Nuclear, Elementary Particle
and High-Energy Physics. 514(1–2), 189–199.'
mla: 'Etesi, Gábor, and Tamás Hausel. “Geometric Construction of New Yang-Mills
Instantons over Taub-NUT Space.” Physics Letters, Section B: Nuclear, Elementary
Particle and High-Energy Physics, vol. 514, no. 1–2, Elsevier, 2001, pp. 189–99,
doi:10.1016/S0370-2693(01)00821-8.'
short: 'G. Etesi, T. Hausel, Physics Letters, Section B: Nuclear, Elementary Particle
and High-Energy Physics 514 (2001) 189–199.'
date_created: 2018-12-11T11:52:07Z
date_published: 2001-08-09T00:00:00Z
date_updated: 2023-05-31T11:51:37Z
day: '09'
doi: 10.1016/S0370-2693(01)00821-8
extern: '1'
external_id:
arxiv:
- hep-th/0105118
intvolume: ' 514'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/hep-th/0105118
month: '08'
oa: 1
oa_version: Preprint
page: 189 - 199
publication: 'Physics Letters, Section B: Nuclear, Elementary Particle and High-Energy
Physics'
publication_identifier:
issn:
- 0370-2693
publication_status: published
publisher: Elsevier
publist_id: '5743'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometric construction of new Yang-Mills instantons over Taub-NUT space
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 514
year: '2001'
...
---
_id: '1454'
abstract:
- lang: eng
text: We address the problem of finding Abelian instantons of finite energy on the
Euclidean Schwarzschild manifold. This amounts to construct self-dual L2 harmonic
2-forms on the space. Gibbons found a non-topological L2 harmonic form in the
Taub-NUT metric, leading to Abelian instantons with continuous energy. We imitate
his construction in the case of the Euclidean Schwarzschild manifold and find
a non-topological self-dual L2 harmonic 2-form on it. We show how this gives rise
to Abelian instantons and identify them with SU(2)-instantons of Pontryagin number
2n2 found by Charap and Duff in 1977. Using results of Dodziuk and Hitchin we
also calculate the full L2 harmonic space for the Euclidean Schwarzschild manifold.
acknowledgement: The work in this paper was done when Tamás Hausel visited the Yukawa
Institute of Kyoto University in February 2000. We are grateful for Prof. G.W. Gibbons
for insightful discussions and Prof. H. Kodama and the Yukawa Institute for the
invitation and hospitality.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Gábor
full_name: Etesi, Gábor
last_name: Etesi
- first_name: Tamas
full_name: Hausel, Tamas
id: 4A0666D8-F248-11E8-B48F-1D18A9856A87
last_name: Hausel
citation:
ama: Etesi G, Hausel T. Geometric interpretation of Schwarzschild instantons. Journal
of Geometry and Physics. 2001;37(1-2):126-136. doi:10.1016/S0393-0440(00)00040-1
apa: Etesi, G., & Hausel, T. (2001). Geometric interpretation of Schwarzschild
instantons. Journal of Geometry and Physics. Elsevier. https://doi.org/10.1016/S0393-0440(00)00040-1
chicago: Etesi, Gábor, and Tamás Hausel. “Geometric Interpretation of Schwarzschild
Instantons.” Journal of Geometry and Physics. Elsevier, 2001. https://doi.org/10.1016/S0393-0440(00)00040-1.
ieee: G. Etesi and T. Hausel, “Geometric interpretation of Schwarzschild instantons,”
Journal of Geometry and Physics, vol. 37, no. 1–2. Elsevier, pp. 126–136,
2001.
ista: Etesi G, Hausel T. 2001. Geometric interpretation of Schwarzschild instantons.
Journal of Geometry and Physics. 37(1–2), 126–136.
mla: Etesi, Gábor, and Tamás Hausel. “Geometric Interpretation of Schwarzschild
Instantons.” Journal of Geometry and Physics, vol. 37, no. 1–2, Elsevier,
2001, pp. 126–36, doi:10.1016/S0393-0440(00)00040-1.
short: G. Etesi, T. Hausel, Journal of Geometry and Physics 37 (2001) 126–136.
date_created: 2018-12-11T11:52:07Z
date_published: 2001-01-01T00:00:00Z
date_updated: 2023-05-31T12:08:45Z
day: '01'
doi: 10.1016/S0393-0440(00)00040-1
extern: '1'
external_id:
arxiv:
- hep-th/0003239
intvolume: ' 37'
issue: 1-2
language:
- iso: eng
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/hep-th/0003239
month: '01'
oa: 1
oa_version: Preprint
page: 126 - 136
publication: Journal of Geometry and Physics
publication_identifier:
issn:
- 0393-0440
publication_status: published
publisher: Elsevier
publist_id: '5744'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Geometric interpretation of Schwarzschild instantons
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 37
year: '2001'
...
---
_id: '9444'
abstract:
- lang: eng
text: Epigenetic silenced alleles of the Arabidopsis SUPERMANlocus (the clark kent
alleles) are associated with dense hypermethylation at noncanonical cytosines
(CpXpG and asymmetric sites, where X = A, T, C, or G). A genetic screen for suppressors
of a hypermethylated clark kent mutant identified nine loss-of-function alleles
of CHROMOMETHYLASE3(CMT3), a novel cytosine methyltransferase homolog. These cmt3
mutants display a wild-type morphology but exhibit decreased CpXpG methylation
of the SUP gene and of other sequences throughout the genome. They also show reactivated
expression of endogenous retrotransposon sequences. These results show that a
non-CpG DNA methyltransferase is responsible for maintaining epigenetic gene silencing.
article_processing_charge: No
article_type: original
author:
- first_name: A. M.
full_name: Lindroth, A. M.
last_name: Lindroth
- first_name: Xiaofeng
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: James P.
full_name: Jackson, James P.
last_name: Jackson
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Claire M.
full_name: McCallum, Claire M.
last_name: McCallum
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Lindroth AM, Cao X, Jackson JP, et al. Requirement of CHROMOMETHYLASE3 for
maintenance of CpXpG methylation. Science. 2001;292(5524):2077-2080. doi:10.1126/science.1059745
apa: Lindroth, A. M., Cao, X., Jackson, J. P., Zilberman, D., McCallum, C. M., Henikoff,
S., & Jacobsen, S. E. (2001). Requirement of CHROMOMETHYLASE3 for maintenance
of CpXpG methylation. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1059745
chicago: Lindroth, A. M., Xiaofeng Cao, James P. Jackson, Daniel Zilberman, Claire
M. McCallum, Steven Henikoff, and Steven E. Jacobsen. “Requirement of CHROMOMETHYLASE3
for Maintenance of CpXpG Methylation.” Science. American Association for
the Advancement of Science, 2001. https://doi.org/10.1126/science.1059745.
ieee: A. M. Lindroth et al., “Requirement of CHROMOMETHYLASE3 for maintenance
of CpXpG methylation,” Science, vol. 292, no. 5524. American Association
for the Advancement of Science, pp. 2077–2080, 2001.
ista: Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen
SE. 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.
Science. 292(5524), 2077–2080.
mla: Lindroth, A. M., et al. “Requirement of CHROMOMETHYLASE3 for Maintenance of
CpXpG Methylation.” Science, vol. 292, no. 5524, American Association for
the Advancement of Science, 2001, pp. 2077–80, doi:10.1126/science.1059745.
short: A.M. Lindroth, X. Cao, J.P. Jackson, D. Zilberman, C.M. McCallum, S. Henikoff,
S.E. Jacobsen, Science 292 (2001) 2077–2080.
date_created: 2021-06-02T13:35:16Z
date_published: 2001-06-15T00:00:00Z
date_updated: 2021-12-14T08:40:32Z
day: '15'
department:
- _id: DaZi
doi: 10.1126/science.1059745
extern: '1'
external_id:
pmid:
- '11349138'
intvolume: ' 292'
issue: '5524'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '06'
oa_version: None
page: 2077-2080
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 292
year: '2001'
...